https://github.com/edoardocostantini/paper-template

My Rnw template for scientific papers

https://github.com/edoardocostantini/paper-template

Repository

My Rnw template for scientific papers

https://github.com/EdoardoCostantini/paper-template/blob/master/

# Project description

Repository hosting the LaTeX manuscript for a paper comparing different MI-PCR specifications.

# Repository contents

This is the template for a LaTex Rnw project. Editing should be done only in the `Rnw` files as the `.tex` are updated based on them upon compilation. 

This directory contains:
- **section_##.Rnw**, the files where the actual content of the paper is written.
- **document_version.Rnw**, the global files calling all the other section files to make up the final manuscript.
- **compile.sh** is a shell script to compile a pdf of any **document_version.Rnw**.
- **trackChanges.sh** is a shell script to obtain track changes pdf versions of the paper
- **makearxiv.sh** is a shell script to create a zip archive that can be uploaded on arxiv.org and compiled by AutoTeX.
- **bib** is the folder containing the .bib file for the bibliography.
- **code** is the folder containing the R scripts defining the plots.
  The scripts for the simulation study plots use plotting functions that are stored in the script `functions.R`.
  - `knit-rnw.R` is the script that prepares the R environment to generate the results to be reported in the paper and knits the document
  - `functions.R` is a script containing possibly complex plotting functions used multiple times in your paper.
  - `sec-study-1-plots.R` contains the call to produce a specific plot to be placed where requested (based on the "title")
- **data** a folder containing the data files to plot
  - `mtcars.rds` is just an example dataset
- **figure** is the folder where the pictures will be stored. You do not need to actively interact with this folder.
- **style** is the folder containing the .cls and .bst files for general formatting of the manuscript.

# How to compile pdfs

## Clean version
You can compile any desired version of the paper using the `compile.sh` bash script.

1. Create a `document_version.Rnw` with the desired latex preamble (style, paper title, authors, etc.)
2. Add calls to the desired sections to include in the manuscript
    - Include `section_##.Rnw` by using
    - Include `section_##.tex` by using
3. Open a terminal window located at the root of the paper folder
4. Execute the following line of code in the terminal
    
. compile.sh document_version.Rnw
    which will create a `document_version.pdf` in the pdf folder.
    For example,
    
. compile.sh main-arxiv.Rnw
    produces the `main-arxiv.pdf` file
## Track-changes versions

After a few commits, you might want to generate a pdf showing the differences between the current version of the paper and any previous one. This can be done easily with the `trackChanges.sh` bash script. To achieve this, run the following command in a terminal window located at the root of the paper folder:
    
. trackChanges.sh document_version.Rnw SHA_old SHA_new 
    which will create a `document_version_diff_SHA_old-SHA_new.pdf` in the pdf folder.
    For example,
    
. trackChanges.sh main-journal.Rnw 12376d19f157d927714aeff0cd1a098a4e087bdd 6c032dc00dede5d862be42fa8f7ae559f7485b5f 
    produces the file:
    `main-journal_diff_12376d19f157d927714aeff0cd1a098a4e087bdd_6c032dc00dede5d862be42fa8f7ae559f7485b5f.pdf`

# Repository structure

Here is the project structure:
```
.
 README.md
 bib
    bibshelf.bib
 code
    functions.R
    knit-rnw.R
    sec-study-1-plots.R
 compile.sh
 data
    mtcars.rds
 figure
    plot-distribution-1.pdf
    plot-mice-1.pdf
    plot-pdf-1.pdf
 main-arxiv.Rnw
 main-arxiv.tex
 main-journal.Rnw
 main-journal.tex
 makearxiv.sh
 pdf
    main-arxiv.pdf
    main-journal.pdf
 sec-abstract.Rnw
 sec-biblio.Rnw
 sec-conclusions.Rnw
 sec-discussion.Rnw
 sec-introduction.Rnw
 sec-limits.Rnw
 sec-methods.Rnw
 sec-study-1.Rnw
 sec-study-2.Rnw
 style
    asj.bst
    response.cls
    sagej.cls
 submissions
 sup-journal.Rnw
 trackChanges.sh
```

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